In case others are having a similar problem, I was receiving Segmentation Fault errors under MPI with gap junctions when I had h.cvode.cache_efficient(1). Under h.cvode.cache_efficient(0), the simulation ran without the error.

I'm working with dendro-dendritic synapses where my pre- cell can have multiple pre-synaptic locations. Depending on section nseg, nearby pre- section(x) locations might be referring to the same segment. When I try to associate multiple gids with a given pre- segment, on the post- end only the synap...

For anyone else who has a similar need to visualize cell model shape beyond what is available in NEURON, I've made tools that I used for such purpose available online. Consider the following options: Use a tool like hoc2swc to convert your cell model to the SWC morphology format. Then you can use an...

Interesting. So it looks like the "orphan root" s2d section was what caused the original problem to appear. The s2d might be safe to remove -- it's only referenced in the create statements, and I found no references to it elsewhere in the project. As you mentioned, it's not connected to anything els...

I noticed another, very similar parent-id-off-by-one issue with another model but now in a single cell instantiation scenario. The underlying cause might be the same. Steps to reproduce: Use this HOC file: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=114665&file=/plast/gc-plast.hoc#t...

I get the same "parent id off-by-one" issue when instantiating multiple instances of a cell made using CellBuilder. Here is the HOC template (soma + a spiraling dendrite): https://pastebin.com/J64KfDmZ Then I instantiate it twice with: h.load_file('TestCell.hoc') c1 = h.TestCell() c2 = h.TestCell() ...

Ah, that's an interesting case. I did notice the two pieces in Shape plot, but I wasn't familiar enough with the model to tell if the oddity was intentional or not. I looked for the "multi-create" issue in the source code of the models that I have locally and was able to find a few other models wher...

I'm running into an issue where when I try to export a model to NeuroML, it generates an XML file that refers to an incorrect parent segment (parent id is off-by-one). Below are the steps to reproduce the issue: # Download a model from ModelDB: https://github.com/ModelDBRepository/116094/archive/mas...

Having gone through the process of proposing the new Stack Exchange site, the main lesson I learned is that proposals for new Stack Exchange sites are more suitable for large communities with high volumes of questions. In general, the broader the topic of a proposed Stack Exchange site, the more lik...

Strangely, writing a post here has made it easier to solve my own problem! The problem appears to be with the NetStim.start time, before the restore, being set to 0. If I set the NetStim.start equal to the h.t value after the restore, the crash dissapears. So I believe I've found a workaround. It is...